New insights into the r/K selection theory achieved in methanogenic systems through continuous-flow and sequencing batch operational modes

Mechanistic understanding of acclimation and energy metabolism of acetoclastic methanogens under different substrate to microorganism ratios

Mechanistic understanding of acetoclastic methanogenesis is pivotal for optimizing anaerobic digestion for efficient methane production. In this study, two different operational modes, continuous flow reactor (CFR) and sequencing batch reactor (SBR), accompanied with solids retention times (SRT) of 10 days (SBR10d and CFR10d) and 25 days (SBR25d and CFR25d) were implemented to elucidate their impacts on microbial communities and energy metabolism of methanogens in acetate-fed systems. Microbial community analysis revealed that the relative abundance of Methanosarcina (16.0%-46.0%) surpassed Methanothrix (3.7%-22.9%) in each reactor. SBRs had the potential to enrich both Methanothrix and Methanosarcina. Compared to SBRs, CFRs had lower total relative abundance of methanogens. Methanosarcina exhibited a superior enrichment in reactors with 10-day SRT, while Methanothrix preferred to be acclimated in reactors with 25-day SRT. The operational mode and SRT were also observed to affect the distribution of acetate-utilizing bacteria, including Pseudomonas, Desulfocurvus, Mesotoga, and Thauera. Regarding enzymes involved in energy metabolism, Ech and Vho/Vht demonstrated higher relative abundances at 10-day SRT compared to 25-day SRT, whereas Fpo and MtrA-H showed higher relative abundances in SBRs than those in CFRs. The relative abundance of genes encoding ATPase harbored by Methanothrix was higher than Methanosarcina at 25-day SRT. Additionally, the relative abundance of V/A-type ATPase (typically for methanogens) was observed higher in SBRs compared to CFRs, while the F-type ATPase (typically for bacteria) exhibited higher relative abundance in CFRs than that in SBRs.

Powdered activated carbon facilitated degradation of complex organic compounds and tetracycline in stressed anaerobic digestion systems

Tetracycline exerts an inhibitory effect on anaerobic digestion, inducing stressed microbial activities and even system failure. Continuous-flow reactors (CFRs) and sequencing batch reactors (SBRs) were employed along with the dosage of powdered activated carbon (PAC) to enhance tetracycline removal during anaerobic digestion of complex organic compounds. PAC increased the maximum methane production rate by 15.6% (CFRs) and 13.8% (SBRs), and tetracycline biodegradation by 24.4% (CFRs) and 19.2% (SBRs). CFRs showed higher tetracycline removal and methane production rates than SBRs. Geobacter was enriched in CFRs, where Methanothrix was enriched with the addition of PAC. Desulfomicrobium harbored abundant propionate degradation-related genes, significantly correlating with tetracycline removal. The genes encoding carbon dioxide reduction in Methanothrix along with the detection of Geobacter might indicate direct interspecies electron transfer for methanogenesis in CFRs and PAC-added reactors. The study offers new insights into anaerobic digestion under tetracycline-stressed conditions and strategies for optimizing tetracycline removal.

Operational mode and powdered activated carbon promoting syntrophic propionate oxidation during anaerobic digestion of complex organic substances

Operational mode and powdered activated carbon (PAC) are key factors facilitating microbial syntrophy and interspecies electron transfer during anaerobic digestion, consequently benefiting process stability and efficient methanogenesis. In this study, continuous-flow reactor (CFR) and sequencing batch reactor (SBR), with and without the addition of PAC, respectively, were operated to examine their effects on system performance and methanogenic activity. Based on the cycle-test result, the PAC-amended CFR (CFRPAC) recorded both the highest methane yield (690.1 mL/L) and the maximum CH4 production rate (28.8 mL/(L·h)), while SBRs exhibited slow methanogenic rates. However, activity assays indicated that SBRs were beneficial for organics removal in batch experiments fed with peptone. Taxonomic and functional analysis confirmed that CFRs were optimal for proliferating oligotrophs (e.g., Geobacter) and SBRs were more suitable for copiotrophs (e.g., Desulfobulbus). Metagenomic analysis revealed that CFRs had efficient acetate metabolic pathways from propionate and ethanol, whereas SBRs did not, resulting in the buildup of propionate. Furthermore, Methanobacterium and Methanothrix were acclimated to the different operational conditions, while acetoclastic Methanosarcina and hydrogenotrophic Methanolinea were acclimated in SBRs (5.1-13.4%) and CFRs (0.3-1.7%), respectively. This study confirmed the enhancement of microbial syntrophy by the addition of PAC as well as the acclimation of electroactive bacteria (e.g., Geobacter) with complex organic substances.

Deciphering anaerobic ethanol metabolic pathways shaped by operational modes

Efficient anaerobic digestion requires the syntrophic cooperation among diverse microorganisms with various metabolic pathways. In this study, two operational modes, i.e., the sequencing batch reactor (SBR) and the continuous-flow reactor (CFR), were adopted in ethanol-fed systems with or without the supplement of powdered activated carbon (PAC) to examine their effects on ethanol metabolic pathways. Notably, the operational mode of SBR and the presence of CO2 facilitated ethanol metabolism towards propionate production. This was further evidenced by the dominance of Desulfobulbus, and the increased relative abundances of enzymes (EC: 1.2.7.1 and 1.2.7.11) involved in CO2 metabolism in SBRs. Moreover, SBRs exhibited superior biomass-based rates of ethanol degradation and methanogenesis, surpassing those in CFRs by 53.1% and 22.3%, respectively. Remarkably, CFRs with the extended solids retention time enriched high relative abundances of Geobacter of 71.7% and 70.4% under conditions with and without the addition of PAC, respectively. Although both long-term and short-term PAC additions led to the increased sludge conductivity and a reduced methanogenic lag phase, only the long-term PAC addition resulted in enhanced rates of ethanol degradation and propionate production/degradation. The strategies by adjusting operational mode and PAC addition could be adopted for modulating the anaerobic ethanol metabolic pathway and enriching Geobacter.

New insights into syntrophic ethanol oxidation: Effects of operational modes and solids retention times

Anaerobic ethanol oxidation relies on syntrophic interactions among functional microorganisms to become thermodynamically feasible. Different operational modes (sequencing batch reactors, SBRs, and continuous flow reactors, CFRs) and solids retention times (SRT, 25 days and 10 days) were employed in four ethanol-fed reactors, named as SBR25d, SBR10d, CFR25d, and CFR10d, respectively. System performance, syntrophic relationships, microbial communities, and metabolic pathways were examined. During the long-term operation, 2002.7 ± 56.0 mg COD/L acetate was accumulated in CFR10d due to the washout of acetotrophic methanogens. Microorganisms with high half-saturation constants were enriched in reactors of 25-day SRT. Moreover, ethanol oxidizing bacteria and acetotrophic methanogens with high half-saturation constants could be acclimated in SBRs. In SBRs, Syner-01 and Methanothrix dominated, and the low SRT of 10 days increased the relative abundance of Geobacter to 38.0%. In CFRs, the low SRT of 10 days resulted in an increase of Desulfovibrio among syntrophic bacteria, and CFR10d could be employed in enriching hydrogenotrophic methanogens like Methanobrevibacter.

Co-digestion of sulfur-rich vegetable waste with waste activated sludge enhanced phosphorus release and hydrogenotrophic methanogenesis

Anaerobic co-digestion of sulfur-rich vegetable waste (SVW) with waste activated sludge (WAS) and the underlying mechanisms associated with methane production and phosphorus (P) release were investigated. Four types of SVW (Chinese cabbage, cabbage, rapeseed cake, and garlic) were utilized for co-digestion with WAS, and the methane yield increased by 7.3%-35.3%; in the meantime, the P release amount from WAS was enhanced by 9.8%-24.9%. The organic carbon in SVW promoted methane production, while organic sulfur and the formation of FeS facilitated P release. Among the four types of SVW, rapeseed cake was identified as the most suitable co-digestion substrate for enhancing both methane production and P release due to its balanced nutrients and relatively high sulfur content. Syntrophic bacteria working with hydrogenotrophic methanogens, iron-reducing bacteria, sulfate-reducing bacteria, and hydrogenotrophic methanogens were enriched. Metabolic pathways related to sulfate reduction and methanogenesis were facilitated, especially hydrogenotrophic methanogenesis. Enzymes involved in hydrogenotrophic methanogenesis were promoted by 76.05%-407.98% with the addition of Chinese cabbage, cabbage, or rapeseed cake. This study provides an eco-friendly technology for promoting P resource and energy recovery from WAS and an in-depth understanding of the corresponding microbial mechanisms.

Pilot-scale two-phase anaerobic digestion of deoiled food waste and waste activated sludge: Effects of mixing ratios and functional analysis

Anaerobic co-digestion of deoiled food waste (dFW) and waste activated sludge (WAS) can address the challenges derived from mono-digestion of FW. In the present study, a pilot-scale methanogenic bioreactor of a two-phase anaerobic digestion system was developed to explore the impact of dFW/WAS volatile solids ratios on the overall performance, microbial community, and metabolic pathways. Besides, the tech-economic of the system was analyzed. The results showed that the degradation efficiency of soluble chemical oxygen demand (SCOD) was more than 84.90% for all the dFW/WAS ratios (v/v) (1:0, 39:1, 29:1, 19:1 and 9:1). Moreover, the dominant genus of bacteria and archaea with different ratios were Lactobacillus (66.84-98.44%) and Methanosaeta (53.66-80.09%), respectively. Co-digestion of dFW and WAS (29: 1 in v/v ratios) obtained the highest yield of methane (0.41 L CH₄/L_added) with approximately 90% of SCOD being removed. In the pilot-scale experiment, the co-digestion of FW and WAS makes positive contribution to reusing solid waste for improving solid management.

Revealing impacts of operational modes on anaerobic digestion systems coupling with sulfate reduction

Anaerobic digestion (AD) is promising for treating high-strength wastewater. However, the effect of operational parameters on microbial communities of AD with sulfate is not yet fully understood. To explore this, four reactors were operated under rapid- and slow-filling modes with different organic carbons. Reactors in the rapid-filling mode generally exhibited a fast kinetic property. For example, the degradation of ethanol was 4.6 times faster in ASBR_ER than in ASBR_ES, and the degradation of acetate was 11.2 times faster in ASBR_AR than in ASBR_AS. Nevertheless, reactors in the slow-filling mode could mitigate propionate accumulation when using ethanol as organic carbon. Taxonomic and functional analysis further supported that rapid- and slow-filling modes were suitable for the growth of r-strategists (e.g., Desulfomicrobium) and K-strategists (e.g., Geobacter), respectively. Overall, this study provides valuable insights into microbial interactions of AD processes with sulfate through the application of the r/K selection theory.

Characterization of the Sediment Bacterial Community Structure and Composition in Najafgarh Lake and Adjoining Dhansa Barrage

This study was undertaken to assess the changes in the community structure, diversity, and composition of sediment bacteria in a shallow lake, Najafgarh Lake (NL), that receives untreated sewage effluent through drains connected to it. These changes were analyzed by comparing the sediment bacterial community structure of NL to the sediment bacterial community structure of Dhansa Barrage (DB), which receives no such effluents. 16S rRNA amplicon was used for bacterial community analysis. Water and sediment samples were also analyzed and compared revealing high conductivity, ammonia, nitrite content, and low dissolved oxygen in NL. The organic matter content is also higher in the sediments of NL. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the predominant phyla in both sites and account for 91% of total bacterial abundance in DB and only 77% in the case of NL. Proteobacteria have the highest relative abundance, accounting for around 42% of the total bacterial population in the case of DB and Firmicutes has the highest relative abundance in Najafgarh at 30%. The diversity analysis found significant differences in the community structure at the two sites. The variation in the bacterial communities in the two wetlands is significantly associated with two water parameters (conductivity and temperature) and two sediment parameters (Sediment Nitrogen and Sediment Organic Matter). Correlation Analysis showed that high ammonia, nitrite, and conductance in NL resulted in bacterial communities shifting towards phyla abundant in degraded ecosystems like Acidobacteria, Choloroflexi, Caldiserica, Aminicenantes, Thaumarchaeota, and Planctomycetes.

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Background

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. 

Results

Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

Conclusion

Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08906-w.

Distribution of extracellular amino acids and their potential functions in microbial cross-feeding in anaerobic digestion systems

Anaerobic digestion is a prevalent bioenergy production process relying on a complex network of symbiotic interactions, where the nutrient based cross-feeding is an essential microbial mechanism. Here, the cross-feeding function was assessed by analyzing extracellular polymeric substances-associated amino acids in microbial aggregates collected from 14 lab-scale anaerobic digesters, as well as deciphering their genetically biosynthetic potential by syntrophic bacteria and methanogens. The total concentration of essential amino acids ranged from 1.2 mg/g VSS to 174.0 mg/g VSS. The percentages of glutamic acid (8.5 ∼ 37.6%), lysine (2.7 ∼ 22.6%), alanine (5.6 ∼ 13.2%), and valine (3.0 ∼ 10.4%) to the total amount of detected amino acids were the highest in most samples. Through metagenomics analysis, several investigated syntrophs (i.e., Smithella, Syntrophobacter, Syntrophomonas, and Mesotoga) and methanogens (i.e., Methanothrix and Methanosarcina) were auxotrophies, but the genetic ability of syntrophs and methanogens to synthesize some essential amino acids could be complementary, implying potential cross-feeding partnership.

The r/K selection theory and its application in biological wastewater treatment processes

Understanding the characteristics of functional organisms is the key to managing and updating biological processes for wastewater treatment. This review, for the first time, systematically characterized two typical types of strategists in wastewater treatment ecosystems via the r/K selection theory and provided novel strategies for selectively enriching microbial community. Functional organisms involved in nitrification (e.g., Nitrosomonas and Nitrosococcus), anammox (Candidatus Brocadia), and methanogenesis (Methanosarcinaceae) are identified as r-strategists with fast growth capacities and low substrate affinities. These r-strategists can achieve high pollutant removal loading rates. On the other hand, other organisms such as Nitrosospira spp., Candidatus Kuenenia, and Methanosaetaceae, are characterized as K-strategists with slow growth rates but high substrate affinities, which can decrease the pollutant concentration to low levels. More importantly, K-strategists may play crucial roles in the biodegradation of recalcitrant organic pollutants. The food-to-microorganism ratio, mass transfer, cell size, and biomass morphology are the key factors determining the selection of r-/K-strategists. These factors can be related with operating parameters (e.g., solids and hydraulic retention time), biomass morphology (biofilm or granules), and operating modes (continuous-flow or sequencing batch), etc., to achieve the efficient acclimation of targeted r-/K-strategists. For practical applications, the concept of substrate flux was put forward to further benefit the selective enrichment of r-/K-strategists, fulfilling effective management and improvement of engineered pollution control bioprocesses. Finally, the future perspectives regarding the development of the r/K selection theory in wastewater treatment processes were discussed.